Thanks for your reply Thomas. I think I'll turn to Tinker since I will
probably need to do several changes in the code in the near future.
Before doing that, I still want to do some TI using Amber. But there are a
few details in the workings of Amber on TI, that I am not sure I correctly
understand. So, can you please tell me if the following procedure is the one
used by Amber:
(L means lambda, DL means delta lambda)
1) V_L = (1-L)V0 + L V1. This is the new Hamiltonian.
2) Run an MD of system V0, with forces scaled by L.
3) Run an MD of system V1, with forces scaled by (1-L).
The simulations above are independent of each other.
4) At a given step in the runs, calculate E_V0 - E_V1 m, divide by DL. This
is the dv/dl that appears in the *.out file.
Questions:
1) L (and 1-L) are applied to every force (on atoms in corresponding masks),
or just to Coulomb and LJ forces?
2) The evolution of each system, V0 and V1, in their own simulation, are
guided only by (1-L)V0 or LV1, respectively, right? In other words, the
Hamiltonian for each simulation is not the whole Hamiltonian V_L, right?
Thanks,
Ignacio
On Tue, Apr 21, 2009 at 11:17 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi Ignacio,
>
> > and try to modify it. Is there any document explaining the logic of the
> > code, what each file does, how the lists of atoms are managed, etc? Or
>
> <insert malicious laughter here> no, there isnt, as far as I know an Amber
> programmers manual doesnt exist. It can be daunting for a beginner to
> modify the code, it may even be easier to switch to something like Tinker
> for what you have in mind. Amber is written to be highly efficient and
> parallel which makes the code fairly complex. It being a group effort of
> many contributors with different programming styles doesn't help
> readability either (but it adds to the fun of working on it :-) )
>
> If you stick to Amber, you could have a look at the call to force() in
> runmd, in the $AMBERHOME/src/sander directory. This is where all the
> interactions are computed. Following the code in force.f will get you to
> the points where all the different interaction types are computed and I
> guess you would have to add exceptions to each of them. A problem would be
> the Ewald routines, as the interaction in the reciprocal part isn't really
> pairwise decomposable.
>
> Overall I would rate what you have in mind to be a fairly complex project
> to get right, but maybe Im overly pessimistic here...
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 12:16:59 PDT
